TL;DR: (The first set of paragraphs is about the main topic of Anora, the first line barrier is about Loghain, and the last is a conclusion)
I really feel we need to be more careful of our time line, because there's clearly discrepancies and different perspectives on how sinister Loghain may or may not have been. Similarly, the actions that you might take can really trip up how you feel about Anora, because of how stark her changes can be, from supporting you with the entirety of her being if she thinks you'll put her on the throne, to horribly, horribly, backstabbing you.
For what its worth, though the main topic clearly has shifted, I find the different developments of Alistair really determined how I felt about who to put on the throne. Before I knew I could harden our bastard prince, I saw a joint marriage as the best logical conclusion, and that I should spare Loghain to aid me in the final battle (it seemed fitting to me). But Alistair's childish reaction demanding that we kill him ("if that's what it takes, I'll become king to see justice done") as his only option to marry Anora, else he would prefer the throne for himself, I was horrified and realized he was in no way qualified to rule the nation.
However, I feel a hardened Alistair was the best choice to rule the nation (not including a joint marriage, again, it makes a great combo if you ask me...) as he had the will to learn the ways of court and his personality did win the day for him.
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That said, back to the time line... Let's look at it for the moment. Your character can theorize with the knight of redcliffe that Eamon was supposed to be poisoned before Cailan even died, and that Loghain might have been planning his grand rebellion for some time. This is supported later when Alistair (hardened) says (when asked about Anora taking the throne) that both Anora and Loghain simply had the ideas they were the only ones who knew how to do things right and, "everyone else, should just stay out of the way."
Keeping in mind that yourself and Duncan needed to travel from wherever they were to Ostagar, Jowan could have been captured relatively early or well after Cailan died, such as the case may be. Even then, it's possible that Loghain was planning on having someone poison Eamon for Maker knows how long, and Jowan's appearance was a convenient happening.
Arl Howe was clearly a scoundrel from the start, but when was it actually clarified whether or not we sided with Loghain from the start or later? Either way, Loghain's willingness to work with such an ambitious traitor is...sketchy, especially to keep on as a second in command. Again, there are also theories that Loghain made the deal with Howe from the very start (whenever the 'start' may be, who knows). Say what you will, Loghain was more than wiling to let Arl Howe torture individuals, and was able to set aside the rights of elves to fund his war. It was his own determination (and paranoia) to push aside the Grey Wardens and the Orlesians, refusing the idea of Alistair being part of the throne as well.
The book "A Game of Thrones" (Which I believe is confirmed as an influence to Gaider and Dragon Age), the Queen goes so far as to order the King not to fight in a tourney, knowing it would enrage him enough that he would most certainly join it. This was all part of her plan so that she could plan his demise in it. Loghain is a smart man, and if we assume he was rather sinister, he may have known that Cailan could be easily manipulated into taking the front lines, and done regardless.
Camera angles and timing (after Cailan declaring it would be a glorious moment) made Loghain seem much more villainous looking back when he says, "Yes....glorious to us all Cailan" (might be paraphrased). So, he could have been planning the retreat for sometime either as a possibility, or a definitive plan from the very start.
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Of course, personally, I believe the game was staged in an ambiguous fashion so that Loghain could be portrayed as both sinister and/or misunderstood. After the course of 4 or so full playthroughs, I've found myself going back and forth several times as to which Loghain was.